Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 3QKLL

Calculation Name: 1D2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q53654

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015498.625967
FMO2-HF: Nuclear repulsion 1941624.921691
FMO2-HF: Total energy -73873.704276
FMO2-MP2: Total energy -74092.96934


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:535:GLU)


Summations of interaction energy for fragment #1(A:535:GLU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-19.54-18.88221.234-10.601-11.2910.112
Interaction energy analysis for fragmet #1(A:535:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.813 / q_NPA : -0.888
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A537THR00.019-0.0033.4537.82410.1310.081-0.869-1.5190.005
4A538SER0-0.013-0.0116.162-4.270-4.2700.0000.0000.0000.000
5A539SER0-0.0090.0019.8350.3830.3830.0000.0000.0000.000
6A540ILE00.0170.01512.809-1.466-1.4660.0000.0000.0000.000
7A541GLY00.0490.03915.6080.3210.3210.0000.0000.0000.000
8A542GLU-1-0.891-0.92919.18614.83814.8380.0000.0000.0000.000
9A543LYS10.7880.91522.914-11.416-11.4160.0000.0000.0000.000
10A544VAL0-0.036-0.01826.210-0.098-0.0980.0000.0000.0000.000
11A545TRP0-0.007-0.01129.064-0.098-0.0980.0000.0000.0000.000
12A546ASP-1-0.861-0.92732.7309.4239.4230.0000.0000.0000.000
13A547ASP-1-0.685-0.81935.1988.7658.7650.0000.0000.0000.000
14A548LYS10.8380.91538.479-7.564-7.5640.0000.0000.0000.000
15A549ASP-1-0.905-0.95437.9498.3708.3700.0000.0000.0000.000
16A550ASN00.0270.02038.710-0.201-0.2010.0000.0000.0000.000
17A551GLN0-0.0200.00140.546-0.208-0.2080.0000.0000.0000.000
18A552ASP-1-0.783-0.85443.6227.0877.0870.0000.0000.0000.000
19A553GLY0-0.044-0.00942.746-0.121-0.1210.0000.0000.0000.000
20A554LYS10.7930.86540.993-7.486-7.4860.0000.0000.0000.000
21A555ARG10.8670.91534.412-9.079-9.0790.0000.0000.0000.000
22A556PRO0-0.0310.00533.961-0.154-0.1540.0000.0000.0000.000
23A557GLU-1-0.866-0.94834.1679.4509.4500.0000.0000.0000.000
24A558LYS10.7540.86929.857-10.485-10.4850.0000.0000.0000.000
25A559VAL00.0000.01327.288-0.333-0.3330.0000.0000.0000.000
26A560SER00.002-0.03026.4760.0580.0580.0000.0000.0000.000
27A561VAL00.0240.03221.306-0.102-0.1020.0000.0000.0000.000
28A562ASN0-0.017-0.04221.4320.2430.2430.0000.0000.0000.000
29A563LEU0-0.018-0.00113.7390.3120.3120.0000.0000.0000.000
30A564LEU00.0070.00117.886-0.251-0.2510.0000.0000.0000.000
31A565ALA00.025-0.01013.0781.4761.4760.0000.0000.0000.000
32A566ASN0-0.055-0.02712.727-0.034-0.0340.0000.0000.0000.000
33A567GLY00.0830.03916.136-0.820-0.8200.0000.0000.0000.000
34A568GLU-1-0.908-0.94017.84113.93013.9300.0000.0000.0000.000
35A569LYS10.8240.91718.022-11.658-11.6580.0000.0000.0000.000
36A570VAL0-0.0010.00614.408-0.299-0.2990.0000.0000.0000.000
37A571LYS10.8510.93712.378-22.791-22.7910.0000.0000.0000.000
38A572THR00.003-0.00818.379-0.062-0.0620.0000.0000.0000.000
39A573LEU0-0.061-0.02518.1210.2400.2400.0000.0000.0000.000
40A574ASP-1-0.764-0.84122.41911.19211.1920.0000.0000.0000.000
41A575VAL0-0.068-0.02423.3010.3880.3880.0000.0000.0000.000
42A576THR00.012-0.04525.890-0.348-0.3480.0000.0000.0000.000
43A577SER00.0180.00228.1800.3640.3640.0000.0000.0000.000
44A578GLU-1-0.893-0.91128.63310.73510.7350.0000.0000.0000.000
45A579THR0-0.052-0.03323.778-0.002-0.0020.0000.0000.0000.000
46A580ASN0-0.061-0.03724.7510.2710.2710.0000.0000.0000.000
47A581TRP00.0030.00826.4870.1560.1560.0000.0000.0000.000
48A582LYS10.8960.95320.691-14.687-14.6870.0000.0000.0000.000
49A583TYR0-0.011-0.02118.232-0.230-0.2300.0000.0000.0000.000
50A584GLU-1-0.824-0.93313.54422.59822.5980.0000.0000.0000.000
51A585PHE0-0.0250.00214.371-0.018-0.0180.0000.0000.0000.000
52A586LYS10.8750.92411.376-20.603-20.6030.0000.0000.0000.000
53A587ASP-1-0.936-0.9668.24629.01029.0100.0000.0000.0000.000
54A588LEU0-0.0280.0028.119-3.102-3.1020.0000.0000.0000.000
55A589PRO00.0440.0244.7136.9537.000-0.001-0.035-0.0100.000
56A590LYS10.8690.9231.651-126.155-128.85718.637-8.553-7.3820.096
57A591TYR0-0.058-0.0392.533-3.309-2.3032.517-1.144-2.3800.011
58A592ASP-1-0.826-0.9205.96822.18722.1870.0000.0000.0000.000
59A593GLU-1-0.937-0.9728.85017.51517.5150.0000.0000.0000.000
60A594GLY0-0.020-0.0018.625-1.105-1.1050.0000.0000.0000.000
61A595LYS10.7930.9149.200-20.773-20.7730.0000.0000.0000.000
62A596LYS10.8250.8827.752-24.311-24.3110.0000.0000.0000.000
63A597ILE0-0.0110.0027.545-3.456-3.4560.0000.0000.0000.000
64A598GLU-1-0.824-0.88610.41923.21823.2180.0000.0000.0000.000
65A599TYR0-0.044-0.0438.345-2.199-2.1990.0000.0000.0000.000
66A600THR00.0080.01014.152-0.177-0.1770.0000.0000.0000.000
67A601VAL0-0.002-0.00117.7940.3580.3580.0000.0000.0000.000
68A602THR00.008-0.00220.367-0.422-0.4220.0000.0000.0000.000
69A603GLU-1-0.738-0.87723.85412.22012.2200.0000.0000.0000.000
70A604ASP-1-0.827-0.88926.62511.69011.6900.0000.0000.0000.000
71A605HIS0-0.049-0.05529.157-0.093-0.0930.0000.0000.0000.000
72A606VAL0-0.0160.00131.596-0.126-0.1260.0000.0000.0000.000
73A607LYS10.7820.85834.477-7.915-7.9150.0000.0000.0000.000
74A608ASP-1-0.867-0.93138.3217.6957.6950.0000.0000.0000.000
75A609TYR0-0.018-0.02634.915-0.103-0.1030.0000.0000.0000.000
76A610THR0-0.013-0.00334.5210.0290.0290.0000.0000.0000.000
77A611THR0-0.020-0.02328.6040.1300.1300.0000.0000.0000.000
78A612ASP-1-0.883-0.94029.68510.91510.9150.0000.0000.0000.000
79A613ILE00.0040.00923.1780.1490.1490.0000.0000.0000.000
80A614ASN0-0.013-0.00723.9530.4540.4540.0000.0000.0000.000
81A615GLY00.0380.02119.8010.2170.2170.0000.0000.0000.000
82A616THR0-0.064-0.06317.5160.8790.8790.0000.0000.0000.000
83A617THR0-0.0100.01019.890-0.228-0.2280.0000.0000.0000.000
84A618ILE0-0.040-0.01422.588-0.266-0.2660.0000.0000.0000.000
85A619THR00.0270.00625.752-0.295-0.2950.0000.0000.0000.000
86A620ASN0-0.051-0.03629.285-0.170-0.1700.0000.0000.0000.000
87A621LYS10.8460.91632.281-10.223-10.2230.0000.0000.0000.000
88A622TYR0-0.064-0.05635.612-0.033-0.0330.0000.0000.0000.000
89A623THR0-0.031-0.01638.742-0.022-0.0220.0000.0000.0000.000
90A624PRO00.0020.01040.890-0.003-0.0030.0000.0000.0000.000
91A625GLY0-0.041-0.02243.532-0.154-0.1540.0000.0000.0000.000
92A626GLU-1-0.963-0.98441.0407.8507.8500.0000.0000.0000.000
93A627THR0-0.0040.00636.6990.2070.2070.0000.0000.0000.000
94A628SER00.0090.01032.741-0.013-0.0130.0000.0000.0000.000
95A629ALA0-0.039-0.01832.944-0.042-0.0420.0000.0000.0000.000
96A630THR00.0030.00326.592-0.080-0.0800.0000.0000.0000.000
97A631VAL0-0.0310.00028.216-0.103-0.1030.0000.0000.0000.000
98A632THR00.0240.00421.4940.1950.1950.0000.0000.0000.000
99A633LYS10.6960.85824.391-11.858-11.8580.0000.0000.0000.000
100A634ASN0-0.008-0.02220.2751.0711.0710.0000.0000.0000.000
101A635TRP0-0.025-0.03320.715-1.127-1.1270.0000.0000.0000.000
102A636ASP-1-0.856-0.91120.31613.37513.3750.0000.0000.0000.000
103A637ASP-1-0.760-0.89420.36513.35813.3580.0000.0000.0000.000
104A638ASN0-0.0300.00018.0260.0300.0300.0000.0000.0000.000
105A639ASN00.0540.02713.7350.5040.5040.0000.0000.0000.000
106A640ASN00.0580.03417.881-1.021-1.0210.0000.0000.0000.000
107A641GLN00.0080.00219.188-0.800-0.8000.0000.0000.0000.000
108A642ASP-1-0.832-0.89021.50410.17210.1720.0000.0000.0000.000
109A643GLY0-0.016-0.01423.766-0.454-0.4540.0000.0000.0000.000
110A644LYS10.7780.87925.090-10.571-10.5710.0000.0000.0000.000
111A645ARG10.8770.95218.983-14.917-14.9170.0000.0000.0000.000
112A646PRO0-0.046-0.01125.825-0.019-0.0190.0000.0000.0000.000
113A647THR00.022-0.01225.2500.3070.3070.0000.0000.0000.000
114A648GLU-1-0.929-0.95825.46911.06211.0620.0000.0000.0000.000
115A649ILE0-0.046-0.01327.713-0.331-0.3310.0000.0000.0000.000
116A650LYS10.9090.96430.003-8.616-8.6160.0000.0000.0000.000
117A651VAL00.0420.01630.700-0.143-0.1430.0000.0000.0000.000
118A652GLU-1-0.833-0.93133.6627.8077.8070.0000.0000.0000.000
119A653LEU00.0200.02734.8540.0660.0660.0000.0000.0000.000
120A654TYR0-0.059-0.03436.908-0.341-0.3410.0000.0000.0000.000
121A655GLN00.0270.00039.324-0.018-0.0180.0000.0000.0000.000
122A656ASP-1-0.811-0.89842.0937.0797.0790.0000.0000.0000.000
123A657GLY00.0000.00542.696-0.185-0.1850.0000.0000.0000.000
124A658LYS10.7730.89244.041-7.158-7.1580.0000.0000.0000.000
125A659ALA00.0730.04342.2170.1690.1690.0000.0000.0000.000
126A660THR0-0.069-0.07040.261-0.119-0.1190.0000.0000.0000.000
127A661GLY0-0.026-0.00542.026-0.085-0.0850.0000.0000.0000.000
128A662LYS10.8700.95137.534-7.996-7.9960.0000.0000.0000.000
129A663THR0-0.032-0.02036.3040.2000.2000.0000.0000.0000.000
130A664ALA00.0250.02431.1600.0510.0510.0000.0000.0000.000
131A665ILE0-0.007-0.00829.361-0.225-0.2250.0000.0000.0000.000
132A666LEU0-0.0200.01526.0550.1920.1920.0000.0000.0000.000
133A667ASN00.0700.02124.5590.2350.2350.0000.0000.0000.000
134A668GLU-1-0.835-0.91318.55316.45716.4570.0000.0000.0000.000
135A669SER0-0.134-0.07920.7430.4220.4220.0000.0000.0000.000
136A670ASN00.0240.00223.2570.1580.1580.0000.0000.0000.000
137A671ASN0-0.013-0.01317.313-0.759-0.7590.0000.0000.0000.000
138A672TRP0-0.058-0.02419.836-0.439-0.4390.0000.0000.0000.000
139A673THR00.0120.00121.829-0.378-0.3780.0000.0000.0000.000
140A674HIS0-0.028-0.01324.447-0.173-0.1730.0000.0000.0000.000
141A675THR00.003-0.00427.8830.1640.1640.0000.0000.0000.000
142A676TRP0-0.056-0.03230.313-0.143-0.1430.0000.0000.0000.000
143A677THR00.0440.00934.1380.0550.0550.0000.0000.0000.000
144A678GLY00.0430.03436.651-0.129-0.1290.0000.0000.0000.000
145A679LEU0-0.061-0.03236.318-0.157-0.1570.0000.0000.0000.000
146A680ASP-1-0.831-0.91240.6837.3587.3580.0000.0000.0000.000
147A681GLU-1-0.720-0.83739.8758.2108.2100.0000.0000.0000.000
148A682LYS10.8390.89442.737-7.021-7.0210.0000.0000.0000.000
149A683ALA00.0630.04146.325-0.056-0.0560.0000.0000.0000.000
150A684LYS10.9110.93849.074-5.909-5.9090.0000.0000.0000.000
151A685GLY00.0540.04551.222-0.112-0.1120.0000.0000.0000.000
152A686GLN0-0.003-0.00348.4190.0460.0460.0000.0000.0000.000
153A687GLN00.0110.01340.202-0.090-0.0900.0000.0000.0000.000
154A688VAL0-0.075-0.01243.030-0.106-0.1060.0000.0000.0000.000
155A689LYS10.8130.87940.004-7.148-7.1480.0000.0000.0000.000
156A690TYR00.002-0.02737.079-0.182-0.1820.0000.0000.0000.000
157A691THR00.0050.01135.4580.0820.0820.0000.0000.0000.000
158A692VAL00.0050.00531.296-0.054-0.0540.0000.0000.0000.000
159A693GLU-1-0.879-0.90434.6378.0568.0560.0000.0000.0000.000
160A694GLU-1-0.754-0.86030.06010.49110.4910.0000.0000.0000.000
161A695LEU0-0.016-0.01034.024-0.219-0.2190.0000.0000.0000.000
162A696THR0-0.028-0.00632.106-0.142-0.1420.0000.0000.0000.000
163A697LYN00.0940.06233.7130.1240.1240.0000.0000.0000.000
164A698VAL00.0190.01328.888-0.066-0.0660.0000.0000.0000.000
165A699LYS10.8530.90332.130-8.104-8.1040.0000.0000.0000.000
166A700GLY00.0310.02031.4150.1270.1270.0000.0000.0000.000
167A701TYR0-0.041-0.04723.9450.0250.0250.0000.0000.0000.000
168A702THR0-0.081-0.02129.907-0.381-0.3810.0000.0000.0000.000
169A703THR00.011-0.00829.7330.3990.3990.0000.0000.0000.000
170A704HIS0-0.0020.00529.559-0.501-0.5010.0000.0000.0000.000
171A705VAL0-0.008-0.01329.6470.3420.3420.0000.0000.0000.000
172A706ASP-1-0.848-0.89328.12210.33910.3390.0000.0000.0000.000
173A707ASN00.022-0.02830.1180.0850.0850.0000.0000.0000.000
174A708ASN0-0.082-0.05231.003-0.496-0.4960.0000.0000.0000.000
175A709ASP-1-0.784-0.87530.10710.18610.1860.0000.0000.0000.000
176A710MET0-0.027-0.01030.9590.1420.1420.0000.0000.0000.000
177A711GLY00.0220.01730.034-0.013-0.0130.0000.0000.0000.000
178A712ASN0-0.003-0.00724.6081.0471.0470.0000.0000.0000.000
179A713LEU0-0.0010.02427.598-0.104-0.1040.0000.0000.0000.000
180A714ILE00.0110.00922.8930.3750.3750.0000.0000.0000.000
181A715THR0-0.022-0.00226.571-0.499-0.4990.0000.0000.0000.000
182A716THR00.004-0.00324.3030.4760.4760.0000.0000.0000.000
183A717ASN0-0.039-0.03825.537-0.416-0.4160.0000.0000.0000.000
184A718LYS10.9430.97225.092-10.078-10.0780.0000.0000.0000.000
185A719TYR0-0.051-0.04825.305-0.691-0.6910.0000.0000.0000.000
186A720THR0-0.068-0.04727.0120.0840.0840.0000.0000.0000.000
187A721PRO0-0.0110.01528.802-0.451-0.4510.0000.0000.0000.000